5,8-Dihydroxy-2,2-dimethyl-12-(3-methylbut-2-enyl)pyrano[3,2-b]xanthen-6-one (brasixanthone B)

The crystal structure of brasixanthone B, a naturally occurring xanthone isolated from the stem bark of Calophyllum gracilentum, is reported. The molecule is characterized by a xanthone skeleton of three fused six-membered rings plus an additional fused pyrano ring and one 3-methylbut-2-enyl side chain.


Synthesis and crystallization
The stem bark (1.2 kg) of calophyllum gracilentum was ground and extracted with n-hexane, chloroform, ethyl acetate and methanol. Fractionation of the hexane extract by gravity column chromatography over (Merck Kieselgel No. 1.09385.1000) silica gel with elution of n-hexane: ethyl acetate and ethyl acetate: methanol in a step-wise gradual increment in polarity. This produced 28 fractions, which were combined and pooled together as 10 sub-fractions based on the TLC profile. Fraction 5 was subjected to further isolation by column chromatography over Sephadex LH20 eluted with methanol and several more purification steps using radial chromatography over silica (Merck Kieselgel No. 1.07749.1000), eluting with an n-hexane:ethyl acetate (8:2) mixture. Yellow needlelike crystals were obtained. The melting point was found to be 500-502 K (Ee et al., 2011).

Figure 2
The crystal packing of brasixanthone B viewed along the b-axis direction. Hydrogen bonds are shown as dashed lines. Hydrogen atoms not involved in hydrogen bonds are omitted for clarity.

Figure 1
The molecular structure of brasixanthone B showing the atomic labeling. Displacement ellipsoids are drawn at the 30% probability level. The intramolecular hydrogen bond is shown as a dashed line.

data-1
IUCrData ( where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max < 0.001 Δρ max = 0.27 e Å −3 Δρ min = −0.24 e Å −3 Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

data-2
IUCrData (2023). 8, x221198 Refinement. The O-bound H atoms were located in a difference map, but fixed during refinement, with distance set to 0.82 Å and U iso (H) = 1.5U eq (O). The remaining H atoms were place in calculated positions with d(C-H) = 0.93 Å for aromatic, 0.97 Å for CH 2 and 0.96 Å for CH 3 atoms. The U iso (H) values were constrained to be 1.5U eq of the carrier atom for methyl H atoms and 1.2U eq for the remaining H atoms.